[BioC] nested model: lme, aov and LSMeans
shirley0818 at gmail.com
Sun Feb 11 17:17:46 CET 2007
I'm working with a nested model (mixed).
I have four factors: Patients, Tissue, sex, and tissue_stage.
Totally I have 10 patients, for each patient, there are 2 tissues
(Cancer vs. Normal).
I think Tissue and sex are fixed. Patient is nested in sex,Tissue is
nested in patient, and tissue_stage is nested in Tissue.
I tried aov and lme as the following,
> aov(gene ~ tissue + gender + patients%in%gender + stage%in%tissue
>lme(gene ~ tissue + gender, random = list(patients = ~1 , stage = ~ 1))
I got results from aov, but I got error message from lme which is
false convergence (8). so I could not compare the results of aov with
Could anybody tell me whether I use the correct command? How can I get
LSMeans for Cancer vs. Normal in R ( I know it is easy in SAS)?
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